Houghton, 45, of Madison was charged two years ago with 47 felony crimes involving allegations that he overprescribed narcotics, failed to adequately monitor patients and inappropriately accepted gifts and cash in exchange for prescriptions.

Gold, reading his decision from the bench, said the charges are far too serious to be resolved through accelerated rehabilitation, a program that would enable Houghton to have the case dismissed if he successfully completes a probationary period.

After listening to testimony in April and reading briefs from prosecutor Russell C. Zentner and defense attorney William F. Dow, Gold said he concluded that “what is alleged here is conduct of an extraordinarily serious nature.” A determination of whether Houghton was prescribing medicine in “good faith,” as required by the law, or in bad faith, “will likely turn on an assessment of Dr. Houghton’s “state of mind,” Gold said. The facts will be subject to interpretation, and “the issue of good faith cannot and should not be resolved, in essence, as a matter of summary judgment.”

The attorneys will resume discussions July 9 in an attempt to resolve the case short of trial.

Houghton has been accompanied by family members and friends at his court appearances, and the judge acknowledged he had received many letters from people who respect Houghton as a physician and a person.

Also attending court appearances have been Houghton’s former partner, Dr. Steven Gaudio of Old Saybrook, drug control agents who investigated the case and family members of Skye Van Epps, a former patient of Houghton’s who died of a drug overdose.

Houghton’s attorney said he was disappointed the judge did not grant the motion but pleased he acknowledged Houghton’s “huge” number of supporters.